She was born an archduchess of Austria as the daughter of Francis II, Holy Roman Emperor, and Maria Theresa of Naples and Sicily.

Born at the Hofburg Palace in Vienna on 1 March 1798, Clementina was the third surviving daughter of Francis II, Holy Roman Emperor, later Emperor Francis I of Austria after the dissolution of the Holy Roman Empire, and his wife Maria Theresa of Naples and Sicily.

From their four children, only a daughter survived to adulthood, Princess Maria Carolina of the Two Sicilies, who on 25 November 1844, in Naples, married her paternal first cousin Prince Henri, Duke of Aumale.

Henri was the fourth (and second-youngest) surviving son of King Louis-Philippe of France and his wife Princess Maria Amalia of Naples and Sicily.

Maria Clementina died on 3 September 1881 at the Château de Chantilly, France, the home of her widowed son-in-law Duke Henri.